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Started by upstream project "BIOFORMATS-test-repo" build number 220 originally caused by: Started by upstream project "Trigger" build number 247 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins1587800976381020302.sh + '[' leica-scn = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_34985_merge_ci -v /uod/idr/repos/curated/leica-scn:/data -v /uod/idr-scratch/merge-ci/curated/leica-scn:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 05:09:10,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:09:10,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 05:09:10,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:09:10,755 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:09:10,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:09:10,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:09:10,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:09:10,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:09:10,757 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:09:10,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:09:10,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:09:10,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:09:10,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:09:10,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:09:11,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:09:11,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:09:11,037 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:09:11,038 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:09:11,038 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:09:11,038 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:09:11,038 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 05:09:11,039 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 05:09:11,039 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 282 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-14 05:09:11,049] [main] java.version = 1.8.0_342 [testng] 05:09:11,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:09:11,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:11,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-14_05-09-11.log] [testng] 05:09:11,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-14 05:09:11,115] [main] testng.directory = /data [testng] [2024-10-14 05:09:11,115] [main] testng.configDirectory = /config [testng] [2024-10-14 05:09:11,134] [main] testng.multiplier = 1.0 [testng] [2024-10-14 05:09:11,134] [main] testng.in-memory = false [testng] [2024-10-14 05:09:11,134] [main] testng.allow-missing = false [testng] [2024-10-14 05:09:11,134] [main] user.language = fr [testng] [2024-10-14 05:09:11,134] [main] user.country = FR [testng] [2024-10-14 05:09:11,134] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-14 05:09:37,288] [main] ---------------------------------------- [testng] [2024-10-14 05:09:37,288] [main] Total files: 12 [testng] [2024-10-14 05:09:37,289] [main] Scan time: 26.153 s (2179 ms/file) [testng] [2024-10-14 05:09:37,289] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-14 05:09:51,893] [pool-1-thread-1] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 fullresolution.jpg: [testng] 05:09:51,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:09:51,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:51,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-14_05-09-51.log] [testng] 05:09:51,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fa90fd1 - End of configuration. [testng] [2024-10-14 05:09:52,041] [pool-1-thread-12] Initializing /data/public/openslide/Leica-1/Leica-1.scn: [testng] 05:09:52,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:09:52,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:52,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-14_05-09-52.log] [testng] 05:09:52,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33e25bb3 - End of configuration. [testng] [2024-10-14 05:09:52,974] [pool-1-thread-11] Initializing /data/qa-11049/HP15.4994_2015-04-28.scn: [testng] 05:09:52,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:09:52,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:52,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-14_05-09-52.log] [testng] 05:09:52,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25569cff - End of configuration. [testng] [2024-10-14 05:09:54,512] [pool-1-thread-10] Initializing /data/public/openslide/Leica-3/Leica-3.scn: [testng] 05:09:54,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:09:54,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:54,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-14_05-09-54.log] [testng] 05:09:54,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39510b57 - End of configuration. [testng] [2024-10-14 05:09:56,231] [pool-1-thread-9] Initializing /data/qa-10469/Slide_907790L_DAPI_Ki67.scn: [testng] 05:09:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:09:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:56,232 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-14_05-09-56.log] [testng] 05:09:56,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@386de963 - End of configuration. [testng] [2024-10-14 05:09:59,921] [pool-1-thread-8] Initializing /data/qa-17671/132223-12_022a1963-b32e-467f-8242-b51a5295951f.SCN: [testng] 05:09:59,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:09:59,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:59,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-14_05-09-59.log] [testng] 05:09:59,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10628999 - End of configuration. [testng] [2024-10-14 05:10:01,134] [pool-1-thread-7] Initializing /data/mihaela/UCLAD_0000000280_2011-02-10 13_32_55Z.scn: [testng] 05:10:01,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:10:01,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:01,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-14_05-10-01.log] [testng] 05:10:01,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4a76d9 - End of configuration. [testng] [2024-10-14 05:10:02,486] [pool-1-thread-6] Initializing /data/scott/Oral_Biology_13 (1).scn: [testng] 05:10:02,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:10:02,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:02,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-14_05-10-02.log] [testng] 05:10:02,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c0e678d - End of configuration. [testng] [2024-10-14 05:10:03,804] [pool-1-thread-5] Initializing /data/public/openslide/Leica-2/Leica-2.scn: [testng] 05:10:03,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:10:03,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:03,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-14_05-10-03.log] [testng] 05:10:03,806 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38d6fa78 - End of configuration. [testng] [2024-10-14 05:10:05,100] [pool-1-thread-4] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46.scn: [testng] 05:10:05,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:10:05,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:05,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-14_05-10-05.log] [testng] 05:10:05,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b31204 - End of configuration. [testng] [2024-10-14 05:10:06,695] [pool-1-thread-3] Initializing /data/scott/ImageCollection_0000000418_2010-10-27 13_31_31Z.scn: [testng] 05:10:06,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:10:06,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:06,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-14_05-10-06.log] [testng] 05:10:06,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bf98546 - End of configuration. [testng] [2024-10-14 05:10:07,758] [pool-1-thread-2] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 opened usig LOCI.tif: [testng] 05:10:07,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:10:07,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:07,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-14_05-10-07.log] [testng] 05:10:07,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a4e3a69 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 636, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 14 seconds Finished: SUCCESS